A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
| Version: | 0.6.5 |
| Depends: | R (≥ 3.5.0), ggplot2 (≥ 3.1.0), dplyr (≥ 0.8.0), dtplyr (≥ 1.0.0), data.table (≥ 1.12.6), patchwork |
| Imports: | factoextra (≥ 1.0.4), fpc, UpSetR (≥ 1.4.0), pheatmap (≥ 1.0.12), ggrepel (≥ 0.8.0), reshape2 (≥ 1.4.2), circlize, MASS (≥ 7.3), Rtsne (≥ 0.15), readr (≥ 1.3.1), readxl (≥ 1.3.1), shiny (≥ 1.4.0), shinythemes, airr, ggseqlogo, stringr (≥ 1.4.0), ggalluvial (≥ 0.10.0), Rcpp (≥ 1.0), magrittr, tibble (≥ 2.0), methods, scales, ggpubr (≥ 0.2), rlang (≥ 0.4), plyr, dbplyr (≥ 1.4.0) |
| LinkingTo: | Rcpp |
| Suggests: | knitr (≥ 1.8), roxygen2 (≥ 3.0.0), testthat (≥ 2.1.0), pkgdown (≥ 0.1.0), assertthat |
| Published: | 2020-06-14 |
| Author: | Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Eugene Rumynskiy [aut], Anna Lorenc [ctb], Daniel J. Moore [ctb], Victor Greiff [ctb], ImmunoMind [cph, fnd] |
| Maintainer: | Vadim I. Nazarov <vdm.nazarov at gmail.com> |
| Contact: | support@immunomind.io |
| BugReports: | https://github.com/immunomind/immunarch/issues |
| License: | AGPL-3 |
| URL: | https://immunarch.com/, https://github.com/immunomind/immunarch |
| NeedsCompilation: | yes |
| Materials: | README NEWS |
| CRAN checks: | immunarch results |
| Reference manual: | immunarch.pdf |
| Vignettes: |
Introduction to immunarch Working with data in immunarch |
| Package source: | immunarch_0.6.5.tar.gz |
| Windows binaries: | r-devel: immunarch_0.6.5.zip, r-release: immunarch_0.6.5.zip, r-oldrel: immunarch_0.6.5.zip |
| macOS binaries: | r-release: immunarch_0.6.5.tgz, r-oldrel: immunarch_0.6.5.tgz |
| Old sources: | immunarch archive |
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